5dgr - Revision history

OCA at 21:41, 28 June 2023

OCA — Wed, 28 Jun 2023 21:41:09 GMT

←Older revision		Revision as of 21:41, 28 June 2023
Line 3:		Line 3:
	<StructureSection load='5dgr' size='340' side='right'caption='[[5dgr]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5dgr' size='340' side='right'caption='[[5dgr]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dgr]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cip_106289 Cip 106289~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DGR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DGR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dgr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Photobacterium_profundum Photobacterium profundum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DGR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=GCS:D~~-~~GLUCOSAMINE'>GCS</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5dgq\|5dgq]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GCS:D-GLUCOSAMINE'>GCS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">VV2739, PBPRA0520 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=74109 CIP 106289])~~</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5dgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dgr OCA], [https://pdbe.org/5dgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dgr RCSB], [https://www.ebi.ac.uk/pdbsum/5dgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dgr ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5dgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dgr OCA], [~~http~~://pdbe.org/5dgr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dgr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dgr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dgr ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6LUT2_PHOPR Q6LUT2_PHOPR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cip 106289]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Fushinobu, S~~]]	+	[[Category: Photobacterium profundum]]
-	[[Category: ~~Honda, Y~~]]	+	[[Category: Fushinobu S]]
-	[[Category: ~~Suzuki, K~~]]	+	[[Category: Honda Y]]
-	[[Category: ~~Alpha-alpha-6 barrel]]~~	+	[[Category: Suzuki K]]
-	~~[[Category: Exo-d-beta-glucosaminidase]]~~	+
-	~~[[Category: Glycoside hydrolase family 9]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:11, 19 February 2020

OCA — Wed, 19 Feb 2020 07:11:48 GMT

←Older revision		Revision as of 07:11, 19 February 2020
Line 1:		Line 1:

	==Crystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520, glucosamine complex==		==Crystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520, glucosamine complex==
-	<StructureSection load='5dgr' size='340' side='right' caption='[[5dgr]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5dgr' size='340' side='right'caption='[[5dgr]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dgr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_106289 Cip 106289]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DGR FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dgr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_106289 Cip 106289]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DGR FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Cip 106289]]		[[Category: Cip 106289]]
		+	[[Category: Large Structures]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]
	[[Category: Honda, Y]]		[[Category: Honda, Y]]

OCA at 13:13, 16 November 2017

OCA — Thu, 16 Nov 2017 13:13:23 GMT

←Older revision		Revision as of 13:13, 16 November 2017
Line 3:		Line 3:
	<StructureSection load='5dgr' size='340' side='right' caption='[[5dgr]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5dgr' size='340' side='right' caption='[[5dgr]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dgr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DGR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dgr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_106289 Cip 106289]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DGR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GCS:D-GLUCOSAMINE'>GCS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GCS:D-GLUCOSAMINE'>GCS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dgq\|5dgq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dgq\|5dgq]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5dgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dgr OCA], [http://pdbe.org/5dgr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dgr RCSB], [http://www.ebi.ac.uk/pdbsum/5dgr PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VV2739, PBPRA0520 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=74109 CIP 106289])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5dgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dgr OCA], [http://pdbe.org/5dgr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dgr RCSB], [http://www.ebi.ac.uk/pdbsum/5dgr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dgr ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cip 106289]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]
	[[Category: Honda, Y]]		[[Category: Honda, Y]]

OCA at 16:04, 10 May 2016

OCA — Tue, 10 May 2016 16:04:29 GMT

←Older revision		Revision as of 16:04, 10 May 2016
Line 1:		Line 1:
		+
	==Crystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520, glucosamine complex==		==Crystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520, glucosamine complex==
	<StructureSection load='5dgr' size='340' side='right' caption='[[5dgr]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5dgr' size='340' side='right' caption='[[5dgr]], [[Resolution\|resolution]] 1.90Å' scene=''>

OCA at 13:40, 9 December 2015

OCA — Wed, 09 Dec 2015 13:40:07 GMT

←Older revision		Revision as of 13:40, 9 December 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520, glucosamine complex==
		+	<StructureSection load='5dgr' size='340' side='right' caption='[[5dgr]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dgr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DGR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GCS:D-GLUCOSAMINE'>GCS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dgq\|5dgq]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5dgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dgr OCA], [http://pdbe.org/5dgr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dgr RCSB], [http://www.ebi.ac.uk/pdbsum/5dgr PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Exo-beta-D-glucosaminidase (EC 3.2.1.165) from Photobacterium profundum (PpGlcNase) is an inverting glycoside hydrolase (GH) belonging to family 9. We have determined the three-dimensional structure of PpGlcNase to describe the first structure-function relationship of an exo-type GH9 glycosidase. PpGlcNase has a narrow and straight active site pocket, in contrast to the long glycan binding cleft of a GH9 endoglucanase. This is because PpGlcNase has a long loop, which blocks the position corresponding to subsites -4 to -2 of the endoglucanase. The pocket shape of PpGlcNase explains its substrate preference for a beta1,4-linkage at the non-reducing terminus. D139, D143 and E555 in the active site were located near the beta-O1 hydroxyl group of GlcN, with D139 and D143 holding a nucleophilic water molecule for hydrolysis. The D139A, D143A and E555A mutants significantly decreased hydrolytic activity, indicating their essential role. Of these mutants, D139A exclusively exhibited glycosynthase activity using alpha-GlcN-F and GlcN as substrates, to produce (GlcN)2. Using saturation mutagenesis at D139, we obtained D139E as the best glycosynthase. Compared with the wild type, the hydrolytic activity of D139E was significantly suppressed (< 0.1%) whereas the fluoride ion-releasing activity also decreased (< 3%). Therefore, the glycosynthase activity of D139E was lower than that of glycosynthases previously created from other inverting GHs. Mutation at the nucleophilic water holder is a general strategy for creating an effective glycosynthase from inverting GHs. However, for GH9, where two acidic residues seem to share the catalytic base role, mutation of D139 might inevitably reduce fluoride ion-releasing activity.

-	The ~~entry 5dgr is ON HOLD until Aug 28 2017~~	+	The crystal structure of an inverting glycoside hydrolase family 9 exo-beta-D-glucosaminidase and the design of glycosynthase.,Honda Y, Arai S, Suzuki K, Kitaoka M, Fushinobu S Biochem J. 2015 Nov 30. pii: BJ20150966. PMID:26621872<ref>PMID:26621872</ref>

-	~~Authors: Suzuki~~, K.~~, Honda, Y., Fushinobu,~~ S.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	<div class="pdbe-citations 5dgr" style="background-color:#fffaf0;"></div>
-	~~[[Category: Unreleased Structures]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]
		+	[[Category: Honda, Y]]
	[[Category: Suzuki, K]]		[[Category: Suzuki, K]]
-	[[Category: ~~Honda, Y~~]]	+	[[Category: Alpha-alpha-6 barrel]]
		+	[[Category: Exo-d-beta-glucosaminidase]]
		+	[[Category: Glycoside hydrolase family 9]]
		+	[[Category: Hydrolase]]

OCA: Protected "5dgr" [edit=sysop:move=sysop]

OCA — Wed, 09 Sep 2015 10:10:33 GMT

Protected "5dgr" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:10, 9 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dgr is ON HOLD until Aug 28 2017 Authors: Suzuki, K., Honda, Y., Fushinobu, S. Description: Category: Unreleased Structures [[Category: Fushi...

OCA — Wed, 09 Sep 2015 10:10:32 GMT

New page: '''Unreleased structure''' The entry 5dgr is ON HOLD until Aug 28 2017 Authors: Suzuki, K., Honda, Y., Fushinobu, S. Description: Category: Unreleased Structures [[Category: Fushi...

New page

'''Unreleased structure'''

The entry 5dgr is ON HOLD until Aug 28 2017

Authors: Suzuki, K., Honda, Y., Fushinobu, S.

Description:
[[Category: Unreleased Structures]]
[[Category: Fushinobu, S]]
[[Category: Suzuki, K]]
[[Category: Honda, Y]]